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    Hspg2 heparan sulfate proteoglycan 2 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 313641, updated on 3-Dec-2024

    Summary

    Symbol
    Hspg2provided by RGD
    Full Name
    heparan sulfate proteoglycan 2provided by RGD
    Primary source
    RGD:621770
    See related
    EnsemblRapid:ENSRNOG00000021437 AllianceGenome:RGD:621770
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Per; AABR07073181.1
    Summary
    Enables collagen V binding activity. Involved in several processes, including animal organ regeneration; embryo implantation; and positive regulation of endothelial cell proliferation. Located in collagen-containing extracellular matrix. Biomarker of hypertension. Human ortholog(s) of this gene implicated in Schwartz-Jampel syndrome 1; Silverman-Handmaker type dyssegmental dysplasia; and osteochondrodysplasia. Orthologous to human HSPG2 (heparan sulfate proteoglycan 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Heart (RPKM 325.9), Adrenal (RPKM 312.2) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Hspg2 in Genome Data Viewer
    Location:
    5q36
    Exon count:
    103
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (154960818..155061971)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (149677437..149778594)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (155812096..155913751)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene chymotrypsin like elastase 3B Neighboring gene RIKEN cDNA 1700013G24 gene like Neighboring gene low density lipoprotein receptor class A domain containing 2 Neighboring gene interferon induced transmembrane protein 2, pseudogene 3

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables axon guidance receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables collagen V binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protease binding ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    involved_in animal organ regeneration IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within brain development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cardiac muscle tissue development ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within cartilage development involved in endochondral bone morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within chondrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in embryo implantation IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    acts_upstream_of_or_within embryonic skeletal system morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within endochondral ossification ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within extracellular matrix organization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of amyloid fibril formation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of cell adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of neuron apoptotic process ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of endothelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within protein localization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in receptor-mediated endocytosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to hypoxia IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to xenobiotic stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in smoothened signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in basement membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in basement membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in collagen-containing extracellular matrix IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular matrix ISO
    Inferred from Sequence Orthology
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    basement membrane-specific heparan sulfate proteoglycan core protein
    Names
    perlecan (heparan sulfate proteoglycan 2)

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001427438.1NP_001414367.1  basement membrane-specific heparan sulfate proteoglycan core protein precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000005
      UniProtKB/TrEMBL
      A0A8I6ASH2
      Related
      ENSRNOP00000097780.1, ENSRNOT00000105209.2

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086023.1 Reference GRCr8

      Range
      154960818..155061971
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039111301.2XP_038967229.1  basement membrane-specific heparan sulfate proteoglycan core protein isoform X1

      UniProtKB/TrEMBL
      A0A8I6ASH2
      Conserved Domains (19) summary
      cd05743
      Location:437514
      Ig_Perlecan_like; Immunoglobulin (Ig)-like domain of the human basement membrane heparan sulfate proteoglycan perlecan and similar proteins
      smart00192
      Location:301332
      LDLa; Low-density lipoprotein receptor domain class A
      smart00408
      Location:28022861
      IGc2; Immunoglobulin C-2 Type
      smart00281
      Location:606732
      LamB; Laminin B domain
      smart00409
      Location:26022679
      IG; Immunoglobulin
      smart00410
      Location:18411921
      IG_like; Immunoglobulin like
      cd00054
      Location:40034036
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      cd00055
      Location:11741223
      EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...
      cd00110
      Location:40894238
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
      cd00112
      Location:384419
      LDLa; Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about ...
      pfam00008
      Location:42634293
      EGF; EGF-like domain
      pfam00052
      Location:10061140
      Laminin_B; Laminin B (Domain IV)
      pfam00053
      Location:12911338
      Laminin_EGF; Laminin EGF domain
      pfam07679
      Location:37313813
      I-set; Immunoglobulin I-set domain
      pfam13927
      Location:33673437
      Ig_3; Immunoglobulin domain
      cd00096
      Location:36623722
      Ig; Immunoglobulin domain
      cd05754
      Location:19292014
      IgI_Perlecan_like; Immunoglobulin (Ig)-like domain found in Perlecan and similar proteins; member of the I-set of Ig superfamily (IgSF) domains
      cl02507
      Location:80194
      SEA; SEA domain
      cl11960
      Location:35603638
      Ig; Immunoglobulin domain
    2. XM_063287775.1XP_063143845.1  basement membrane-specific heparan sulfate proteoglycan core protein isoform X3

      UniProtKB/TrEMBL
      A0A8I6A2S5, A0A8I6ASH2
      Related
      ENSRNOP00000086030.1, ENSRNOT00000098496.2
    3. XM_063287774.1XP_063143844.1  basement membrane-specific heparan sulfate proteoglycan core protein isoform X2

      UniProtKB/TrEMBL
      A0A8I6ASH2
    4. XM_063287776.1XP_063143846.1  basement membrane-specific heparan sulfate proteoglycan core protein isoform X4

      UniProtKB/TrEMBL
      A0A8I6ASH2